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Dharni JS, Shi Y, Zhang C, Petersen C, Walia H, Staswick P. Growth and transcriptional response of wheat and rice to the tertiary amine BMVE. FRONTIERS IN PLANT SCIENCE 2024; 14:1273620. [PMID: 38269141 PMCID: PMC10806070 DOI: 10.3389/fpls.2023.1273620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 12/04/2023] [Indexed: 01/26/2024]
Abstract
Introduction Seed vigor is largely a product of sound seed development, maturation processes, genetics, and storage conditions. It is a crucial factor impacting plant growth and crop yield and is negatively affected by unfavorable environmental conditions, which can include drought and heat as well as cold wet conditions. The latter leads to slow germination and increased seedling susceptibility to pathogens. Prior research has shown that a class of plant growth regulators called substituted tertiary amines (STAs) can enhance seed germination, seedling growth, and crop productivity. However, inconsistent benefits have limited STA adoption on a commercial scale. Methods We developed a novel seed treatment protocol to evaluate the efficacy of 2-(N-methyl benzyl aminoethyl)-3-methyl butanoate (BMVE), which has shown promise as a crop seed treatment in field trials. Transcriptomic analysis of rice seedlings 24 h after BMVE treatment was done to identify the molecular basis for the improved seedling growth. The impact of BMVE on seed development was also evaluated by spraying rice panicles shortly after flower fertilization and subsequently monitoring the impact on seed traits. Results BMVE treatment of seeds 24 h after imbibition consistently improved wheat and rice seedling shoot and root growth in lab conditions. Treated wheat seedlings grown to maturity in a greenhouse also resulted in higher biomass than controls, though only under drought conditions. Treated seedlings had increased levels of transcripts involved in reactive oxygen species scavenging and auxin and gibberellic acid signaling. Conversely, several genes associated with increased reactive oxygen species/ROS load, abiotic stress responses, and germination hindering processes were reduced. BMVE spray increased both fresh and mature seed weights relative to the control for plants exposed to 96 h of heat stress. BMVE treatment during seed development also benefited germination and seedling growth in the next generation, under both ambient and heat stress conditions. Discussion The optimized experimental conditions we developed provide convincing evidence that BMVE does indeed have efficacy in plant growth enhancement. The results advance our understanding of how STAs work at the molecular level and provide insights for their practical application to improve crop growth.
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Affiliation(s)
- Jaspinder Singh Dharni
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
| | - Yu Shi
- School of Biological Sciences, University of Nebraska, Lincoln, NE, United States
| | - Chi Zhang
- School of Biological Sciences, University of Nebraska, Lincoln, NE, United States
| | | | - Harkamal Walia
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
| | - Paul Staswick
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
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Dash PK, Rai R, Pradhan SK, Shivaraj SM, Deshmukh R, Sreevathsa R, Singh NK. Drought and Oxidative Stress in Flax ( Linum usitatissimum L.) Entails Harnessing Non-Canonical Reference Gene for Precise Quantification of qRT-PCR Gene Expression. Antioxidants (Basel) 2023; 12:antiox12040950. [PMID: 37107326 PMCID: PMC10136167 DOI: 10.3390/antiox12040950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Flax (Linum usitatissimum L.) is a self-pollinating, annual, diploid crop grown for multi-utility purposes for its quality oil, shining bast fiber, and industrial solvent. Being a cool (Rabi) season crop, it is affected by unprecedented climatic changes such as high temperature, drought, and associated oxidative stress that, globally, impede its growth, production, and productivity. To precisely assess the imperative changes that are inflicted by drought and associated oxidative stress, gene expression profiling of predominant drought-responsive genes (AREB, DREB/CBF, and ARR) was carried out by qRT-PCR. Nevertheless, for normalization/quantification of data obtained from qRT-PCR results, a stable reference gene is mandatory. Here, we evaluated a panel of four reference genes (Actin, EF1a, ETIF5A, and UBQ) and assessed their suitability as stable reference genes for the normalization of gene expression data obtained during drought-induced oxidative stress in flax. Taking together, from the canonical expression of the proposed reference genes in three different genotypes, we report that EF1a as a stand-alone and EF1a and ETIF5A in tandem are suitable reference genes to be used for the real-time visualization of cellular impact of drought and oxidative stress on flax.
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Affiliation(s)
- Prasanta K Dash
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Rhitu Rai
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Sharat Kumar Pradhan
- ICAR-National Rice Research Institute, Cuttack 753006, India
- Indian Council of Agricultural Research, Krishi Bhawan, New Delhi 110012, India
| | | | - Rupesh Deshmukh
- Department of Biotechnology, Central University of Haryana, Mahendragarh 123031, India
| | - Rohini Sreevathsa
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Nagendra K Singh
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
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Vlaminck L, De Rouck B, Desmet S, Van Gerrewey T, Goeminne G, De Smet L, Storme V, Kyndt T, Demeestere K, Gheysen G, Inzé D, Vanholme B, Depuydt S. Opposing effects of trans- and cis-cinnamic acid during rice coleoptile elongation. PLANT DIRECT 2022; 6:e465. [PMID: 36545006 PMCID: PMC9763633 DOI: 10.1002/pld3.465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 10/29/2022] [Accepted: 11/01/2022] [Indexed: 06/17/2023]
Abstract
The phenylpropanoid cinnamic acid (CA) is a plant metabolite that can occur under a trans- or cis-form. In contrast to the proven bioactivity of the cis-form (c-CA), the activity of trans-CA (t-CA) is still a matter of debate. We tested both compounds using a submerged rice coleoptile assay and demonstrated that they have opposite effects on cell elongation. Notably, in the tip of rice coleoptile t-CA showed an inhibiting and c-CA a stimulating activity. By combining transcriptomics and (untargeted) metabolomics with activity assays and genetic and pharmacological experiments, we aimed to explain the underlying mechanistic processes. We propose a model in which c-CA treatment activates proton pumps and stimulates acidification of the apoplast, which in turn leads to the loosening of the cell wall, necessary for elongation. We hypothesize that c-CA also inactivates auxin efflux transporters, which might cause a local auxin accumulation in the tip of the coleoptile. For t-CA, the phenotype can partially be explained by a stimulation of cell wall polysaccharide feruloylation, leading to a more rigid cell wall. Metabolite profiling also demonstrated that salicylic acid (SA) derivatives are increased upon t-CA treatment. As SA is a known antagonist of auxin, the shift in SA homeostasis provides an additional explanation of the observed t-CA-mediated restriction on cell growth.
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Affiliation(s)
- Lena Vlaminck
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB‐UGent Center for Plant Systems BiologyGhentBelgium
- Laboratory of Plant Growth AnalysisGhent University Global CampusIncheonSouth Korea
| | - Brix De Rouck
- Laboratory of Plant Growth AnalysisGhent University Global CampusIncheonSouth Korea
| | | | - Thijs Van Gerrewey
- Laboratory of Plant Growth AnalysisGhent University Global CampusIncheonSouth Korea
| | | | - Lien De Smet
- Department of BiotechnologyGhent UniversityGhentBelgium
| | - Veronique Storme
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB‐UGent Center for Plant Systems BiologyGhentBelgium
| | - Tina Kyndt
- Department of BiotechnologyGhent UniversityGhentBelgium
| | - Kristof Demeestere
- Department of Green Chemistry and TechnologyGhent UniversityGhentBelgium
| | | | - Dirk Inzé
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB‐UGent Center for Plant Systems BiologyGhentBelgium
| | - Bartel Vanholme
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB‐UGent Center for Plant Systems BiologyGhentBelgium
| | - Stephen Depuydt
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB‐UGent Center for Plant Systems BiologyGhentBelgium
- Laboratory of Plant Growth AnalysisGhent University Global CampusIncheonSouth Korea
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4
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Zeng H, Chen X, Li H, Zhang J, Wei Z, Wang Y. Interpopulation differences of retroduplication variations (RDVs) in rice retrogenes and their phenotypic correlations. Comput Struct Biotechnol J 2021; 19:600-611. [PMID: 33510865 PMCID: PMC7811064 DOI: 10.1016/j.csbj.2020.12.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/29/2020] [Accepted: 12/31/2020] [Indexed: 11/21/2022] Open
Abstract
Retroduplication variation (RDV), a type of retrocopy polymorphism, is considered to have essential biological significance, but its effect on gene function and species phenotype is still poorly understood. To this end, we analyzed the retrocopies and RDVs in 3,010 rice genomes. We calculated the RDV frequencies in the genome of each rice population; detected the mutated, ancestral and expressed retrogenes in rice genomes; and analyzed their RDV influence on rice phenotypic traits. Collectively, 73 RDVs were identified, and 14 RDVs in ancestral retrogenes can significantly affect rice phenotypes. Our research reveals that RDV plays an important role in rice migration, domestication and evolution. We think that RDV is a good molecular breeding marker candidate. To our knowledge, this is the first study on the relationship between retrogene function, expression, RDV and species phenotype.
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Affiliation(s)
- Haiyue Zeng
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
- Biological Science Research Center, Southwest University, Chongqing 400715, China
- Shennong Class, Southwest University, Chongqing 400715, China
| | - Xingyu Chen
- Shennong Class, Southwest University, Chongqing 400715, China
| | - Hongbo Li
- College of Electronic and Information Engineering, Southwest University, Chongqing 400715
| | - Jun Zhang
- College of Computer & Information Science, Southwest University, Chongqing 400715, China
| | - Zhaoyuan Wei
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
- Biological Science Research Center, Southwest University, Chongqing 400715, China
| | - Yi Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
- Biological Science Research Center, Southwest University, Chongqing 400715, China
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5
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Nghi KN, Tagliani A, Mariotti L, Weits DA, Perata P, Pucciariello C. Auxin is required for the long coleoptile trait in japonica rice under submergence. THE NEW PHYTOLOGIST 2021; 229:85-93. [PMID: 32609884 DOI: 10.1111/nph.16781] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 06/20/2020] [Indexed: 06/11/2023]
Abstract
Rice coleoptile elongation under submergence guarantees fast seedling establishment in the field. We investigated the role of auxin in influencing the capacity of rice to produce a long coleoptile under water. In order to explore the complexity of auxin's role in coleoptile elongation, we used gene expression analysis, confocal microscopy of an auxin-responsive fluorescent reporter, gas chromatography coupled to tandem mass spectrometry (GC-MS/MS), and T-DNA insertional mutants of an auxin transport protein. We show that a higher auxin availability in the coleoptile correlates with the final coleoptile length under submergence. We also identified the auxin influx carrier AUX1 as a component influencing this trait under submergence. The coleoptile tip is involved in the final length of rice varieties harbouring a long coleoptile. Our experimental results indicate that auxin biosynthesis and transport underlies the differential elongation between short and long coleoptile-harbouring japonica rice varieties.
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Affiliation(s)
- Khac Nhu Nghi
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Andrea Tagliani
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
- nanoPlant Centre @NEST, Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Lorenzo Mariotti
- Department of Agriculture, Food and Environment, University of Pisa, Italy
| | - Daan A Weits
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
- nanoPlant Centre @NEST, Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Pierdomenico Perata
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
- nanoPlant Centre @NEST, Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Chiara Pucciariello
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
- nanoPlant Centre @NEST, Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
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6
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Müller JT, van Veen H, Bartylla MM, Akman M, Pedersen O, Sun P, Schuurink RC, Takeuchi J, Todoroki Y, Weig AR, Sasidharan R, Mustroph A. Keeping the shoot above water - submergence triggers antithetical growth responses in stems and petioles of watercress (Nasturtium officinale). THE NEW PHYTOLOGIST 2021; 229:140-155. [PMID: 31792981 DOI: 10.1111/nph.16350] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/26/2019] [Indexed: 05/25/2023]
Abstract
The molecular mechanisms controlling underwater elongation are based extensively on studies on internode elongation in the monocot rice (Oryza sativa) and petiole elongation in Rumex rosette species. Here, we characterize underwater growth in the dicot Nasturtium officinale (watercress), a wild species of the Brassicaceae family, in which submergence enhances stem elongation and suppresses petiole growth. We used a genome-wide transcriptome analysis to identify the molecular mechanisms underlying the observed antithetical growth responses. Though submergence caused a substantial reconfiguration of the petiole and stem transcriptome, only little qualitative differences were observed between both tissues. A core submergence response included hormonal regulation and metabolic readjustment for energy conservation, whereas tissue-specific responses were associated with defense, photosynthesis, and cell wall polysaccharides. Transcriptomic and physiological characterization suggested that the established ethylene, abscisic acid (ABA), and GA growth regulatory module for underwater elongation could not fully explain underwater growth in watercress. Petiole growth suppression is likely attributed to a cell cycle arrest. Underwater stem elongation is driven by an early decline in ABA and is not primarily mediated by ethylene or GA. An enhanced stem elongation observed in the night period was not linked to hypoxia and suggests an involvement of circadian regulation.
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Affiliation(s)
- Jana T Müller
- Plant Physiology, University Bayreuth, Universitaetsstraße 30, 95440, Bayreuth, Germany
| | - Hans van Veen
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Malte M Bartylla
- Plant Physiology, University Bayreuth, Universitaetsstraße 30, 95440, Bayreuth, Germany
| | - Melis Akman
- Plant and Microbial Biology, University of California, Berkeley, 361 Koshland Hall, Berkeley, CA, 94720, USA
- Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Ole Pedersen
- Department of Biology, University of Copenhagen, Universitetsparken 4, 2100, Copenhagen, Denmark
| | - Pulu Sun
- Green Life Sciences Research Cluster, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH, Amsterdam, the Netherlands
| | - Robert C Schuurink
- Green Life Sciences Research Cluster, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH, Amsterdam, the Netherlands
| | - Jun Takeuchi
- Faculty of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Yasushi Todoroki
- Faculty of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Alfons R Weig
- Genomics & Bioinformatics, University Bayreuth, Universitaetsstraße 30, 95440, Bayreuth, Germany
| | - Rashmi Sasidharan
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Angelika Mustroph
- Plant Physiology, University Bayreuth, Universitaetsstraße 30, 95440, Bayreuth, Germany
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7
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Molecular Mechanisms Supporting Rice Germination and Coleoptile Elongation under Low Oxygen. PLANTS 2020; 9:plants9081037. [PMID: 32824201 PMCID: PMC7465159 DOI: 10.3390/plants9081037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/09/2020] [Accepted: 08/10/2020] [Indexed: 12/28/2022]
Abstract
Rice germinates under submergence by exploiting the starch available in the endosperm and translocating sugars from source to sink organs. The availability of fermentable sugar under water allows germination with the protrusion of the coleoptile, which elongates rapidly and functions as a snorkel toward the air above. Depending on the variety, rice can produce a short or a long coleoptile. Longer length entails the involvement of a functional transport of auxin along the coleoptile. This paper is an overview of rice coleoptiles and the studies undertaken to understand its functioning and role under submergence.
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Rohilla M, Singh N, Mazumder A, Sen P, Roy P, Chowdhury D, Singh NK, Mondal TK. Genome-wide association studies using 50 K rice genic SNP chip unveil genetic architecture for anaerobic germination of deep-water rice population of Assam, India. Mol Genet Genomics 2020; 295:1211-1226. [PMID: 32506235 DOI: 10.1007/s00438-020-01690-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/19/2020] [Indexed: 12/13/2022]
Abstract
North Eastern part of India such as Assam is inundated by flood every year where the farmers are forced to grow the traditional tall deep-water rice. Genetic improvement of this type of rice is slow because of insufficient knowledge about their genetic architecture and population structure. In the present investigation, the genetic diversity architecture of 94 deep-water rice genotypes of Assam and association mapping strategy was, for the first time, applied to determine the significant SNPs and genes for deep-water rice. These genotypes are known for their unique elongation ability under deep-water condition. The anaerobic germination (AG) related trait-associated genes identified here can provide affluent resources for rice breeding especially in flood-prone areas. We investigated the genome-wide association studies (GWAS) using 50 K rice genic SNP chip across 94 deep-water rice genotypes collected from different flood-prone districts/villages of Assam. Population structure and diversity analysis revealed that these genotypes were stratified into four sub-populations. Using GWAS approach, 20 significant genes were identified and found to be associated with AG-related traits. Of them, two most relevant genes (OsXDH1and SSXT) have been identified which explain phenotypic variability (R2 > 20%) in the population. These genes were located in Chr 3 (LOC_Os03g31550) which encodes for enzyme xanthine dehydrogenase 1(OsXDH1) and in Chr 12 (LOC_Os12g31350) which encodes for SSXT family protein. Both of these genes were found to be associated with anaerobic response index (increase in the coleoptile length under water in anaerobic condition with respect to control), respectively. Interestingly, OsXDH1is involved in purine catabolism pathway and acts as a scavenger of reactive oxygen species in plants, whereas SSXT is GRF1-interacting factor 3. These two candidate genes associated with AG of deep-water rice have been found to be reported for the first time. Thus, this study provides a greater resource for breeders not only for improvement of deep-water rice, but also for AG tolerant variety useful for direct-seeded rice in flood-affected areas.
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Affiliation(s)
- Megha Rohilla
- ICAR-National Institute for Plant Biotechnology, Pusa, New Delhi, 110012, India
| | - Nisha Singh
- ICAR-National Institute for Plant Biotechnology, Pusa, New Delhi, 110012, India
| | - Abhishek Mazumder
- ICAR-National Institute for Plant Biotechnology, Pusa, New Delhi, 110012, India
| | - Priyabrata Sen
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Priyanka Roy
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Dhiren Chowdhury
- Regional Agricultural Research Station, Assam Agricultural University, North Lakhimpur, Assam, India
| | | | - Tapan Kumar Mondal
- ICAR-National Institute for Plant Biotechnology, Pusa, New Delhi, 110012, India.
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Wang HQ, Liu P, Zhang JW, Zhao B, Ren BZ. Endogenous Hormones Inhibit Differentiation of Young Ears in Maize ( Zea mays L.) Under Heat Stress. FRONTIERS IN PLANT SCIENCE 2020; 11:533046. [PMID: 33193473 PMCID: PMC7642522 DOI: 10.3389/fpls.2020.533046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 10/06/2020] [Indexed: 05/10/2023]
Abstract
Global warming frequently leads to extreme temperatures, which pose a serious threat to the growth, development, and yield formation of crops such as maize. This study aimed to deeply explore the molecular mechanisms of young ear development under heat stress. We selected the heat-tolerant maize variety Zhengdan 958 (T) and heat-sensitive maize variety Xianyu 335 (S), and subjected them to heat stress in the V9 (9th leaf), V12 (12th leaf), and VT (tasseling) growth stages. We combined analysis of the maize phenotype with omics technology and physiological indicators to compare the differences in young ear morphology, total number of florets, floret fertilization rate, grain abortion rate, number of grains, and main metabolic pathways between plants subjected to heat stress and those left to develop normally. The results showed that after heat stress, the length and diameter of young ears, total number of florets, floret fertilization rate, and number of grains all decreased significantly, whereas the length of the undeveloped part at the top of the ear and grain abortion rate increased significantly. In addition, the differentially expressed genes (DEGs) in young ears were significantly enriched in the hormone signaling pathways. The endogenous hormone content in young ears exhibited different changes: zeatin (ZT) and zeatin riboside (ZR) decreased significantly, but gibberellin acid3 (GA3), gibberellin acid4 (GA4), and abscisic acid (ABA) increased significantly, in ears subjected to heat stress. In the heat-tolerant maize variety, the salicylic acid (SA), and jasmonic acid (JA) content in the vegetative growth stage also increased in ears subjected to heat stress, whereas the opposite effect was observed for the heat-sensitive variety. The changes in endogenous hormone content of young ears that were subjected to heat stress significantly affected ear development, resulting in a reduction in the number of differentiated florets, fertilized florets and grains, which ultimately reduced the maize yield.
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Vlaminck L, Sang-Aram C, Botterman D, Uy CJC, Harper MK, Inzé D, Gheysen G, Depuydt S. Development of a novel and rapid phenotype-based screening method to assess rice seedling growth. PLANT METHODS 2020; 16:139. [PMID: 33072175 PMCID: PMC7560306 DOI: 10.1186/s13007-020-00682-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 10/07/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND Rice (Oryza sativa) is one of the most important model crops in plant research. Despite its considerable advantages, (phenotypic) bioassays for rice are not as well developed as for Arabidopsis thaliana. Here, we present a phenotype-based screening method to study shoot-related parameters of rice seedlings via an automated computer analysis. RESULTS The phenotype-based screening method was validated by testing several compounds in pharmacological experiments that interfered with hormone homeostasis, confirming that the assay was consistent with regard to the anticipated plant growth regulation and revealing the robustness of the set-up in terms of reproducibility. Moreover, abiotic stress tests using NaCl and DCMU, an electron transport blocker during the light dependent reactions of photosynthesis, confirmed the validity of the new method for a wide range of applications. Next, this method was used to screen the impact of semi-purified fractions of marine invertebrates on the initial stages of rice seedling growth. Certain fractions clearly stimulated growth, whereas others inhibited it, especially in the root, illustrating the possible applications of this novel, robust, and fast phenotype-based screening method for rice. CONCLUSIONS The validated phenotype-based and cost-efficient screening method allows a quick and proper analysis of shoot growth and requires only small volumes of compounds and media. As a result, this method could potentially be used for a whole range of applications, ranging from discovery of novel biostimulants, plant growth regulators, and plant growth-promoting bacteria to analysis of CRISPR knockouts, molecular plant breeding, genome-wide association, and phytotoxicity studies. The assay system described here can contribute to a better understanding of plant development in general.
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Affiliation(s)
- Lena Vlaminck
- Present Address: Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Laboratory of Plant Growth Analysis, Ghent University Global Campus, Incheon, 21985 South Korea
| | - Chananchida Sang-Aram
- Present Address: Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Laboratory of Plant Growth Analysis, Ghent University Global Campus, Incheon, 21985 South Korea
| | - Deborah Botterman
- Laboratory of Plant Growth Analysis, Ghent University Global Campus, Incheon, 21985 South Korea
| | - Christine Jewel C. Uy
- Laboratory of Plant Growth Analysis, Ghent University Global Campus, Incheon, 21985 South Korea
| | - Mary Kay Harper
- Department of Medical Chemistry, University of Utah, Salt Lake City, UT 84112 USA
| | - Dirk Inzé
- Present Address: Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | | | - Stephen Depuydt
- Present Address: Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Laboratory of Plant Growth Analysis, Ghent University Global Campus, Incheon, 21985 South Korea
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11
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Nghi KN, Tondelli A, Valè G, Tagliani A, Marè C, Perata P, Pucciariello C. Dissection of coleoptile elongation in japonica rice under submergence through integrated genome-wide association mapping and transcriptional analyses. PLANT, CELL & ENVIRONMENT 2019; 42:1832-1846. [PMID: 30802973 DOI: 10.1111/pce.13540] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 02/06/2019] [Accepted: 02/10/2019] [Indexed: 05/23/2023]
Abstract
Rice is unique among cereals for its ability to germinate not only when submerged but also under anoxic conditions. Rice germination under submergence or anoxia is characterized by a longer coleoptile and delay in radicle emergence. A panel of temperate and tropical japonica rice accessions showing a large variability in coleoptile length was used to investigate genetic factors involved in this developmental process. The ability of the Khao Hlan On rice landrace to vigorously germinate when submerged has been previously associated with the presence of the trehalose 6 phosphate phosphatase 7 (TPP7) gene. In this study, we found that, in the presence of TPP7, polymorphisms and transcriptional variations of the gene in coleoptile tissue were not related to differences in the final coleoptile length under submergence. In order to find new chromosomal regions associated with the different ability of rice to elongate the coleoptile under submergence, we used genome-wide association study analysis on a panel of 273 japonica rice accessions. We discovered 11 significant marker-trait associations and identified candidate genes potentially involved in coleoptile length. Candidate gene expression analyses indicated that japonica rice genotypes possess complex genetic elements that control final coleoptile length under low oxygen.
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Affiliation(s)
- Khac Nhu Nghi
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Alessandro Tondelli
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Giampiero Valè
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Vercelli, Italy
| | - Andrea Tagliani
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Caterina Marè
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Pierdomenico Perata
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Chiara Pucciariello
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
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12
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Chu Y, Xu N, Wu Q, Yu B, Li X, Chen R, Huang J. Rice transcription factor OsMADS57 regulates plant height by modulating gibberellin catabolism. RICE (NEW YORK, N.Y.) 2019; 12:38. [PMID: 31139953 PMCID: PMC6538746 DOI: 10.1186/s12284-019-0298-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 05/16/2019] [Indexed: 05/08/2023]
Abstract
BACKGROUND The MADS-box transcription factors mainly function in floral organ organogenesis and identity specification. Few research on their roles in vegetative growth has been reported. RESULTS Here we investigated the functions of OsMADS57 in plant vegetative growth in rice (Oryza sativa). Knockdown of OsMADS57 reduced the plant height, internode elongation and panicle exsertion in rice plants. Further study showed that the cell length was remarkably reduced in the uppermost internode in OsMADS57 knockdown plants at maturity. Moreover, OsMADS57 knockdown plants were more sensitive to gibberellic acid (GA3), and contained less bioactive GA3 than wild-type plants, which implied that OsMADS57 is involved in gibberellin (GA) pathway. Expectedly, the transcript levels of OsGA2ox3, encoding GAs deactivated enzyme, were significantly enhanced in OsMADS57 knockdown plants. The level of EUI1 transcripts involved in GA deactivation was also increased in OsMADS57 knockdown plants. More importantly, dual-luciferase reporter assay and electrophoretic mobility shift assay showed that OsMADS57 directly regulates the transcription of OsGA2ox3 as well as EUI1 through binding to the CArG-box motifs in their promoter regions. In addition, OsMADS57 also modulated the expression of multiple genes involved in GA metabolism or GA signaling pathway, indicating the key and complex regulatory role of OsMADS57 in GA pathway in rice. CONCLUSIONS These results indicated that OsMADS57 acts as an important transcriptional regulator that regulates stem elongation and panicle exsertion in rice via GA-mediated regulatory pathway.
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Affiliation(s)
- Yanli Chu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
| | - Ning Xu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
| | - Qi Wu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
| | - Bo Yu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
| | - Xingxing Li
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
| | - Rongrong Chen
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
| | - Junli Huang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
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13
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Yuan Y, Zhang Q, Zeng S, Gu L, Si W, Zhang X, Tian D, Yang S, Wang L. Selective sweep with significant positive selection serves as the driving force for the differentiation of japonica and indica rice cultivars. BMC Genomics 2017; 18:307. [PMID: 28420345 PMCID: PMC5395770 DOI: 10.1186/s12864-017-3702-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 04/08/2017] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Asian cultivated rice (Oryza sativa L.), including japonica and indica, is unarguable the most important crop in Asia as well as worldwide. However, a decisive conclusion of its origination and domestication processes are still lacking. Nowadays, the ever-increasing high-throughput sequencing data of numerous rice samples have provided us new opportunities to get close to the answer of these questions. RESULTS By compiling 296 whole-genome sequenced rice cultivars and 39 diverse wild rice, two types of domesticated regions (DR-I and DR-II) with strong selective sweep signals between different groups were detected. DR-I regions included 28 blocks which significantly differentiated between japonica and indica subspecies, while DR-II regions were consisted of another 28 blocks which significantly differentiated between wild and cultivated rice, each covered 890 kb and 640 kb, respectively. In-depth analysis suggested that both DR-Is and DR-IIs could have originated from Indo-China Peninsula to southern China, and DR-IIs might be introgressed from indica to japonica. Functional bias with significant positive selection has also been detected in the genes of DR-I, suggesting important role of the selective sweep in differentiation of japonica and indica. CONCLUSIONS This research promoted a new possible model of the origin of the cultivated rice that DR-Is in japonica and indica maybe independently originated from the divergent wild rice in the Indo-China Peninsula to southern China, and then followed by frequent introgression. Genes with significant positive selection and biased functions were also detected which could play important roles in rice domestication and differentiation processes.
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Affiliation(s)
- Yang Yuan
- The Applied Plant Genomics Laboratory, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, China
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Qijun Zhang
- Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Shuiyun Zeng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Longjiang Gu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Weina Si
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xiaohui Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Dacheng Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
| | - Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
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14
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Guo F, Han N, Xie Y, Fang K, Yang Y, Zhu M, Wang J, Bian H. The miR393a/target module regulates seed germination and seedling establishment under submergence in rice (Oryza sativa L.). PLANT, CELL & ENVIRONMENT 2016; 39:2288-302. [PMID: 27342100 DOI: 10.1111/pce.12781] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 06/09/2016] [Accepted: 06/12/2016] [Indexed: 05/23/2023]
Abstract
The conserved miRNA393 family is thought to be involved in root elongation, leaf development and stress responses, but its role during seed germination and seedling establishment remains unclear. In this study, expression of the MIR393a/target module and its role in germinating rice (Oryza sativa L.) seeds were investigated. β-Glucuronidase (GUS) analysis showed that MIR393a and OsTIR1 had spatial-temporal transcriptional activities in radicle roots, coleoptile tips and stomata cells, corresponding to a dynamic auxin response. miR393a promoted primary root elongation when rice seeds were germinated in air and inhibited coleoptile elongation and stomatal development when seeds were submerged. Under submergence, the expression of miR393a was inhibited, and then the auxin response was induced. In the process, OsTIR1 and OsAFB2, auxin receptor genes, were negatively regulated by miR393. We found that miR393a inhibited stomatal development and coleoptile elongation but promoted free indole acetic acid (IAA) accumulation in the rice coleoptile tips. In addition, exogenous abscisic acid (ABA) enhanced the expression of miR393 and inhibited coleoptile growth. Together, miR393a/target plays a role in coleoptile elongation and stomatal development via modulation of auxin signalling during seed germination and seedling establishment under submergence. This study provides new perspectives on the direct sowing of rice seeds in flooded paddy fields.
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Affiliation(s)
- Fu Guo
- Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Ning Han
- Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Yakun Xie
- Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Ke Fang
- Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Yinong Yang
- Department of Plant Pathology and Huck Institutes of Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Muyuan Zhu
- Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Junhui Wang
- Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
| | - Hongwu Bian
- Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
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15
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Liu Y, Zhang J, Li W, Guo C, Shu Y. In silicoidentification, phylogeny and expression analysis of expansin superfamily in Medicago truncatula. BIOTECHNOL BIOTEC EQ 2015. [DOI: 10.1080/13102818.2015.1093919] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
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16
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Geilfus CM, Ober D, Eichacker LA, Mühling KH, Zörb C. Down-regulation of ZmEXPB6 (Zea mays β-expansin 6) protein is correlated with salt-mediated growth reduction in the leaves of Z. mays L. J Biol Chem 2015; 290:11235-45. [PMID: 25750129 DOI: 10.1074/jbc.m114.619718] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 11/06/2022] Open
Abstract
The salt-sensitive crop Zea mays L. shows a rapid leaf growth reduction upon NaCl stress. There is increasing evidence that salinity impairs the ability of the cell walls to expand, ultimately inhibiting growth. Wall-loosening is a prerequisite for cell wall expansion, a process that is under the control of cell wall-located expansin proteins. In this study the abundance of those proteins was analyzed against salt stress using gel-based two-dimensional proteomics and two-dimensional Western blotting. Results show that ZmEXPB6 (Z. mays β-expansin 6) protein is lacking in growth-inhibited leaves of salt-stressed maize. Of note, the exogenous application of heterologously expressed and metal-chelate-affinity chromatography-purified ZmEXPB6 on growth-reduced leaves that lack native ZmEXPB6 under NaCl stress partially restored leaf growth. In vitro assays on frozen-thawed leaf sections revealed that recombinant ZmEXPB6 acts on the capacity of the walls to extend. Our results identify expansins as a factor that partially restores leaf growth of maize in saline environments.
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Affiliation(s)
- Christoph-Martin Geilfus
- From the Institute of Plant Nutrition and Soil Science, Christian-Albrechts-University, Hermann-Rodewald-Strasse 2, 24118 Kiel, Germany,
| | - Dietrich Ober
- Botanical Institute and Botanical Gardens, Biochemical Ecology and Molecular Evolution, Christian-Albrechts-University, Am Botanischen Garten 1-9, 24118 Kiel, Germany
| | - Lutz A Eichacker
- Universitetet i Stavanger, Center for Organelle Research (CORE), Richard Johnsensgt. 4, N-4021, Norway, and
| | - Karl Hermann Mühling
- From the Institute of Plant Nutrition and Soil Science, Christian-Albrechts-University, Hermann-Rodewald-Strasse 2, 24118 Kiel, Germany
| | - Christian Zörb
- From the Institute of Plant Nutrition and Soil Science, Christian-Albrechts-University, Hermann-Rodewald-Strasse 2, 24118 Kiel, Germany, Institute of Crop Science, Quality of Plant Products, University Hohenheim, Schloss, Westhof West, 118, 70593 Stuttgart, Germany
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17
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Li X, Zhao J, Walk TC, Liao H. Characterization of soybean β-expansin genes and their expression responses to symbiosis, nutrient deficiency, and hormone treatment. Appl Microbiol Biotechnol 2014; 98:2805-17. [PMID: 24113821 DOI: 10.1007/s00253-013-5240-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 08/15/2013] [Accepted: 08/18/2013] [Indexed: 01/21/2023]
Abstract
Expansins are plant cell wall-loosening proteins encoded by a superfamily of genes including α-expansin, β-expansin, expansin-like A, and expansin-like B proteins. They play a variety of biological roles during plant growth and development. Expansin genes have been reported in many plant species, and results primarily from graminaceous members indicate that β-expansins are more abundant in monocots than in dicots. Soybean [Glycine max (L.) Merr] is an important legume crop. This work identified nine β-expansin gene family members in soybean (GmEXPBs) that were divided into two distinct classes based on phylogeny and gene structure, with divergence between the two groups occurring more in introns than in exons. A total of 887 hormone-responsive and environmental stress-related putative cis-elements from 188 families were found in the 2-kb upstream region of GmEXPBs. Variations in number and type of cis-elements associated with each gene indicate that the function of these genes is differentially regulated by these signals. Expression analysis confirmed that the family members were ubiquitously, yet differentially expressed in soybean. Responsiveness to nutrient deficiency stresses and regulation by auxin (indole-3-acetic acid) and cytokinin (6-benzylaminopurine) varied among GmEXPBs. In addition, most β-expansin genes were associated with symbiosis of soybean inoculated with Rhizobium or abuscular mycorrhizal fungi (AMF). Taken together, these results systematically investigate the characteristics of the entire GmEXPB family in soybean and comprise the first report analyzing the relationship of GmEXPBs with rhizobial or AMF symbiosis. This information is a valuable step in the process of understanding the expansin protein functions in soybean and opens avenues for continued researches.
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Affiliation(s)
- Xinxin Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Root Biology Center, South China Agricultural University, Guangzhou, People's Republic of China
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18
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Galli V, da Silva Messias R, dos Anjos e Silva SD, Rombaldi CV. Selection of reliable reference genes for quantitative real-time polymerase chain reaction studies in maize grains. PLANT CELL REPORTS 2013; 32:1869-77. [PMID: 24013792 DOI: 10.1007/s00299-013-1499-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 07/25/2013] [Accepted: 08/26/2013] [Indexed: 05/03/2023]
Abstract
The stability of candidate reference genes was evaluated in maize landrace varieties and during multiple grain developmental stages to evaluate the expression of carotenoid-related genes by RT-qPCR for application to maize biofortification. Vitamin A deficiency affects millions of children worldwide; therefore, increasing the content of vitamin A precursors in maize grains is of interest. The study of the expression of genes involved in the carotenoid biosynthetic pathway in maize grains has provided useful information for metabolic engineering approaches. However, reliable results using real-time quantitative polymerase chain reaction (RT-qPCR) experiments are dependent on the use of the appropriate reference genes. In this study, we utilized geNorm and NormFinder softwares to identify the most stably expressed candidate reference genes in samples from seven stages of grain development and from eight landrace varieties. The results of the analysis performed using geNorm indicated that tubulin (TUB) and actin (ACT) were the most suitable reference genes among all experimental conditions, while glyceraldehyde-3-phosphate dehydrogenase gene (GAPDH) showed the least stability. The same result was obtained with the NormFinder software. The minimum number of genes required in each experimental condition to normalize the gene expression data was also determined by geNorm. The expression of phytoene synthase gene (PSY1), the first enzyme in the carotenoid biosynthetic pathway, was overestimated when the least stable candidate gene (GAPDH) was used as the internal control instead of the most stable gene pair (ACT + TUB), thus highlighting the importance of validating reference genes before conducting a RT-qPCR experiment to obtain accurate results. This study is the first survey of the stability of genes for use as reference genes to normalize RT-qPCR data from maize landraces during multiple stages of grain development.
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Affiliation(s)
- Vanessa Galli
- Empresa Brasileira de Pesquisa Agropecuária de Clima Temperado, Rodovia BR 396, Km 78 Postal code 403, Pelotas, RS, CEP 96001-970, Brazil,
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19
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Azuma T, Inoue Y, Hamada Y, Okishio T, Sasayama D, Itoh K. Anoxia promotes gravitropic curvature in rice pulvini but inhibits it in wheat and oat pulvini. JOURNAL OF PLANT PHYSIOLOGY 2013; 170:1158-64. [PMID: 23591078 DOI: 10.1016/j.jplph.2013.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 03/15/2013] [Accepted: 03/21/2013] [Indexed: 05/17/2023]
Abstract
Gravitropic curvature of pulvini of wheat and oat stem segments gradually declined with decreasing atmospheric O₂ concentration and was almost completely blocked under anoxia, whereas that of rice stem segments was enhanced under hypoxia and anoxia. Anoxia substantially increased the ethanol content in pulvini of gravistimulated stem segments in rice, wheat and oat, but the ethanol content showed no marked difference between rice pulvini and wheat and oat pulvini. The concentrations of exogenous ethanol and acetaldehyde required to inhibit the gravitropic curvature of pulvini were significantly higher in rice segments than in wheat and oat segments. However, in all three species, the concentrations of ethanol and acetaldehyde required to completely inhibit curvature were several-fold higher than the endogenous levels that accumulated in pulvini gravistimulated in N₂. The pulvini of rice segments gravistimulated in N₂ did not contain much more ATP than those of wheat or oat segments gravistimulated in N₂. When applied unilaterally to the pulvini of vertically oriented stem segments incubated in N₂, indole-3-acetic acid induced bending in rice stem segments but not in wheat and oat stem segments. Transference of graviresponsive pulvini of rice, as well as those of wheat and oat, from aerobic conditions to anaerobic conditions led to cessation of gravitropic curvature within several minutes, but subsequently only gravitropic curvature of anoxic rice pulvini was completely recovered within 2 h. A large portion of this recovery was blocked by cordycepin, a transcription inhibitor. These results suggested that anoxia-induced expression of any gene or genes enables rice pulvini to respond to gravistimulation under anaerobic conditions, and that such a gene or genes might be unrelated to ethanol fermentation and ATP production in anaerobic conditions.
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Affiliation(s)
- Tetsushi Azuma
- Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe 657-8501, Japan.
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20
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Matilla AJ, Rodríguez-Gacio MDC. Non-symbiotic hemoglobins in the life of seeds. PHYTOCHEMISTRY 2013; 87:7-15. [PMID: 23286879 DOI: 10.1016/j.phytochem.2012.11.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 11/13/2012] [Accepted: 11/21/2012] [Indexed: 06/01/2023]
Abstract
Non-symbiotic hemoglobins (nsHbs), ancestors of symbiotic-Hbs, are hexacoordinated dimeric proteins, for which the crystal structure is well described. According to the extent of hexacoordination, nsHbs are classified as belonging to class-1 (nsHbs1) or class-2 (nsHbs2). The nsHbs1 show weak hexacoordination, moderate rates of O(2)-binding, very small rates of O(2) dissociation, and a remarkably high affinity for O(2), all suggesting a function involving O(2) scavenging. In contrast, the nsHbs2 exhibit strong hexacoordination, low rates of O(2)-binding and moderately low O(2) dissociation and affinity, suggesting a sensing role for sustained low (μM) levels of O(2). The existence of spatial and specific expression of nsHbs1 suggests that nsHbs play tissue-specific rather than housekeeping functions. The permeation of O(2) into seeds is usually prevented during the desiccation phase and early imbibition, generating an internal hypoxic environment that leads to ATP limitation. During evolution, the seed has acquired mechanisms to prevent or reduce this hypoxic stress. The nsHbs1/NO cycle appear to be involved in modulating the redox state in the seed and in maintaining an active metabolism. Under O(2) deficit, NADH and NO are synthesized in the seed and nsHbs1 scavenges O(2), which is used to transform NO into NO(3)(-) with concomitant formation of Fe(3+)-nsHbs1. Expression of nsHbs1 is not detectable in dry viable seeds. However, in the seeds cross-talk occurs between nsHbs1 and NO during germination. This review considers the current status of our knowledge of seed nsHbs and considers key issues of further work to better understand their role in seed physiology.
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Affiliation(s)
- Angel J Matilla
- Department of Plant Physiology, University of Santiago de Compostela, 15782 Santiago de Compostela, A Coruña, Spain.
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21
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Banti V, Giuntoli B, Gonzali S, Loreti E, Magneschi L, Novi G, Paparelli E, Parlanti S, Pucciariello C, Santaniello A, Perata P. Low oxygen response mechanisms in green organisms. Int J Mol Sci 2013; 14:4734-61. [PMID: 23446868 PMCID: PMC3634410 DOI: 10.3390/ijms14034734] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 02/20/2013] [Accepted: 02/21/2013] [Indexed: 01/04/2023] Open
Abstract
Low oxygen stress often occurs during the life of green organisms, mostly due to the environmental conditions affecting oxygen availability. Both plants and algae respond to low oxygen by resetting their metabolism. The shift from mitochondrial respiration to fermentation is the hallmark of anaerobic metabolism in most organisms. This involves a modified carbohydrate metabolism coupled with glycolysis and fermentation. For a coordinated response to low oxygen, plants exploit various molecular mechanisms to sense when oxygen is either absent or in limited amounts. In Arabidopsis thaliana, a direct oxygen sensing system has recently been discovered, where a conserved N-terminal motif on some ethylene responsive factors (ERFs), targets the fate of the protein under normoxia/hypoxia. In Oryza sativa, this same group of ERFs drives physiological and anatomical modifications that vary in relation to the genotype studied. The microalga Chlamydomonas reinhardtii responses to low oxygen seem to have evolved independently of higher plants, posing questions on how the fermentative metabolism is modulated. In this review, we summarize the most recent findings related to these topics, highlighting promising developments for the future.
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Affiliation(s)
- Valeria Banti
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant’Anna, Via Mariscoglio 34, Pisa 56124, Italy; E-Mails: (V.B.); (B.G.); (S.G.); (G.N.); (E.P.); (S.P.); (C.P.); (A.S.)
| | - Beatrice Giuntoli
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant’Anna, Via Mariscoglio 34, Pisa 56124, Italy; E-Mails: (V.B.); (B.G.); (S.G.); (G.N.); (E.P.); (S.P.); (C.P.); (A.S.)
| | - Silvia Gonzali
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant’Anna, Via Mariscoglio 34, Pisa 56124, Italy; E-Mails: (V.B.); (B.G.); (S.G.); (G.N.); (E.P.); (S.P.); (C.P.); (A.S.)
| | - Elena Loreti
- Institute of Agricultural Biology and Biotechnology, National Research Council, Via Moruzzi 1, Pisa 56100, Italy; E-Mail:
| | - Leonardo Magneschi
- Institute of Plant Biochemistry and Biotechnology, University of Münster, Schlossplatz 8, Münster 48143, Germany; E-Mail:
| | - Giacomo Novi
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant’Anna, Via Mariscoglio 34, Pisa 56124, Italy; E-Mails: (V.B.); (B.G.); (S.G.); (G.N.); (E.P.); (S.P.); (C.P.); (A.S.)
| | - Eleonora Paparelli
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant’Anna, Via Mariscoglio 34, Pisa 56124, Italy; E-Mails: (V.B.); (B.G.); (S.G.); (G.N.); (E.P.); (S.P.); (C.P.); (A.S.)
| | - Sandro Parlanti
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant’Anna, Via Mariscoglio 34, Pisa 56124, Italy; E-Mails: (V.B.); (B.G.); (S.G.); (G.N.); (E.P.); (S.P.); (C.P.); (A.S.)
| | - Chiara Pucciariello
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant’Anna, Via Mariscoglio 34, Pisa 56124, Italy; E-Mails: (V.B.); (B.G.); (S.G.); (G.N.); (E.P.); (S.P.); (C.P.); (A.S.)
| | - Antonietta Santaniello
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant’Anna, Via Mariscoglio 34, Pisa 56124, Italy; E-Mails: (V.B.); (B.G.); (S.G.); (G.N.); (E.P.); (S.P.); (C.P.); (A.S.)
| | - Pierdomenico Perata
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant’Anna, Via Mariscoglio 34, Pisa 56124, Italy; E-Mails: (V.B.); (B.G.); (S.G.); (G.N.); (E.P.); (S.P.); (C.P.); (A.S.)
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Rice phytochrome-interacting factor-like protein OsPIL1 functions as a key regulator of internode elongation and induces a morphological response to drought stress. Proc Natl Acad Sci U S A 2012; 109:15947-52. [PMID: 22984180 DOI: 10.1073/pnas.1207324109] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The mechanisms for plant growth restriction during stress conditions remains unclear. Here, we demonstrate that a phytochrome-interacting factor-like protein, OsPIL1/OsPIL13, acts as a key regulator of reduced internode elongation in rice under drought conditions. The level of OsPIL1 mRNA in rice seedlings grown under nonstressed conditions with light/dark cycles oscillated in a circadian manner with peaks in the middle of the light period. Under drought stress conditions, OsPIL1 expression was inhibited during the light period. We found that OsPIL1 was highly expressed in the node portions of the stem using promoter-glucuronidase analysis. Overexpression of OsPIL1 in transgenic rice plants promoted internode elongation. In contrast, transgenic rice plants with a chimeric repressor resulted in short internode sections. Alteration of internode cell size was observed in OsPIL1 transgenic plants, indicating that differences in cell size cause the change in internode length. Oligoarray analysis revealed OsPIL1 downstream genes, which were enriched for cell wall-related genes responsible for cell elongation. These data suggest that OsPIL1 functions as a key regulatory factor of reduced plant height via cell wall-related genes in response to drought stress. This regulatory system may be important for morphological stress adaptation in rice under drought conditions.
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Takahashi H, Saika H, Matsumura H, Nagamura Y, Tsutsumi N, Nishizawa NK, Nakazono M. Cell division and cell elongation in the coleoptile of rice alcohol dehydrogenase 1-deficient mutant are reduced under complete submergence. ANNALS OF BOTANY 2011; 108:253-61. [PMID: 21788375 PMCID: PMC3143047 DOI: 10.1093/aob/mcr137] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 04/06/2011] [Indexed: 05/04/2023]
Abstract
BACKGROUND AND AIMS When rice seeds germinate under complete submergence, only the coleoptile elongates efficiently. It has been reported previously that coleoptile elongation is reduced in the rice alcohol dehydrogenase 1 (ADH1)-deficient mutant, reduced adh activity (rad). The aim of this study was to elucidate how expressions of genes responsible for coleoptile elongation are affected by the ADH1 deficiency in the rad mutant under submergence. METHODS To identify genes whose expressions are changed in the rad coleoptile at an early stage in germination (i.e. 1 d after imbibition), coleoptiles of the rad mutant and its wild type (WT) were isolated by laser microdissection, and their mRNA levels were examined with a microarray. KEY RESULTS The microarray analysis identified 431 genes whose transcript levels were different between rad and WT. Interestingly, among the down-regulated genes in the rad coleoptile, 17·5 % were cell division-related genes and 5·1 % were cell elongation-related genes. It was found that cell division started at 1 d after imbibition and then gradually ceased, whereas in the WT coleoptile cell elongation started between 1 d and 2 d after imbibition and then continued. However, neither cell division nor cell elongation actively occurred in the rad coleoptile, in which the amounts of ATP were reduced. CONCLUSIONS These results indicate that cell division, as well as cell elongation, occur during coleoptile elongation in rice under complete submergence, and that the reduced ATP levels caused by the ADH1 deficiency repress both of them, thereby impairing coleoptile elongation in the rad mutant under submerged conditions.
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Affiliation(s)
- Hirokazu Takahashi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Hiroaki Saika
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Hideo Matsumura
- Gene Research Center, Shinshu University, 3-15-1 Tokita, Ueda, Nagano 386-8567, Japan
| | - Yoshiaki Nagamura
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Nobuhiro Tsutsumi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Naoko K. Nishizawa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Nonoichimachi, Ishikawa 921-8836, Japan
| | - Mikio Nakazono
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601, Japan
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Koizumi Y, Hara Y, Yazaki Y, Sakano K, Ishizawa K. Involvement of plasma membrane H+-ATPase in anoxic elongation of stems in pondweed (Potamogeton distinctus) turions. THE NEW PHYTOLOGIST 2011; 190:421-430. [PMID: 21232059 DOI: 10.1111/j.1469-8137.2010.03605.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
• Pondweed (Potamogeton distinctus) turions can elongate in the absence of O(2). Alcoholic fermentation serves to produce energy for anoxic elongation via the breakdown of starch stored in cells. However, the mechanism of cell growth during anoxic elongation is not fully understood. • Changes in pH, H(+) equivalent and lactate content of the incubation medium were measured during anoxic elongation. The effects of fusicoccin (FC), indole-3-acetic acid (IAA), vanadate, erythrosine B and K(+) channel blockers on anoxic elongation were examined. Cytoplasmic pH and vacuolar pH were measured by (31)P nuclear magnetic resonance (NMR) spectroscopy. • Acidification of the incubation medium occurred during anoxic elongation. The contribution of CO(2) and lactic acid was not sufficient to explain the acidification. FC and IAA enhanced the elongation of stem segments. Vanadate and erythrosine B inhibited anoxic elongation. Acid growth of notched segments was observed. The activity of plasma membrane H(+)-ATPase extracted from pondweed turions was increased slightly in anoxic conditions, but that from pea epicotyls sensitive to anoxic conditions was decreased by incubation in anoxic conditions. Both the cytoplasmic pH and vacuolar pH of pondweed turion cells chased by (32)P NMR spectroscopy were stabilized during a short period < 3 h after anoxic conditions. • We propose that the enhancement of H(+) extrusion by anoxic conditions induces acidification in the apoplast and may contribute to the stabilization of pH in the cytoplasm.
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Affiliation(s)
- Yayoi Koizumi
- Biological Institute, Graduate School of Science, Tohoku University, Sendai, Japan
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Huis R, Hawkins S, Neutelings G. Selection of reference genes for quantitative gene expression normalization in flax (Linum usitatissimum L.). BMC PLANT BIOLOGY 2010; 10:71. [PMID: 20403198 PMCID: PMC3095345 DOI: 10.1186/1471-2229-10-71] [Citation(s) in RCA: 159] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Accepted: 04/19/2010] [Indexed: 05/20/2023]
Abstract
BACKGROUND Quantitative real-time PCR (qRT-PCR) is currently the most accurate method for detecting differential gene expression. Such an approach depends on the identification of uniformly expressed 'housekeeping genes' (HKGs). Extensive transcriptomic data mining and experimental validation in different model plants have shown that the reliability of these endogenous controls can be influenced by the plant species, growth conditions and organs/tissues examined. It is therefore important to identify the best reference genes to use in each biological system before using qRT-PCR to investigate differential gene expression. In this paper we evaluate different candidate HKGs for developmental transcriptomic studies in the economically-important flax fiber- and oil-crop (Linum usitatissimum L). RESULTS Specific primers were designed in order to quantify the expression levels of 20 different potential housekeeping genes in flax roots, internal- and external-stem tissues, leaves and flowers at different developmental stages. After calculations of PCR efficiencies, 13 HKGs were retained and their expression stabilities evaluated by the computer algorithms geNorm and NormFinder. According to geNorm, 2 Transcriptional Elongation Factors (TEFs) and 1 Ubiquitin gene are necessary for normalizing gene expression when all studied samples are considered. However, only 2 TEFs are required for normalizing expression in stem tissues. In contrast, NormFinder identified glyceraldehyde-3-phosphate dehydrogenase (GADPH) as the most stably expressed gene when all samples were grouped together, as well as when samples were classed into different sub-groups.qRT-PCR was then used to investigate the relative expression levels of two splice variants of the flax LuMYB1 gene (homologue of AtMYB59). LuMYB1-1 and LuMYB1-2 were highly expressed in the internal stem tissues as compared to outer stem tissues and other samples. This result was confirmed with both geNorm-designated- and NormFinder-designated-reference genes. CONCLUSIONS The use of 2 different statistical algorithms results in the identification of different combinations of flax HKGs for expression data normalization. Despite such differences, the use of geNorm-designated- and NormFinder-designated-reference genes enabled us to accurately compare the expression levels of a flax MYB gene in different organs and tissues. Our identification and validation of suitable flax HKGs will facilitate future developmental transcriptomic studies in this economically-important plant.
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Affiliation(s)
- Rudy Huis
- UMR INRA-USTL 1281 Stress Abiotiques et Différenciation des Végétaux Cultivés, Bât. SN2, Université Lille 1, F-59655 Villeneuve d'Ascq, France
| | - Simon Hawkins
- UMR INRA-USTL 1281 Stress Abiotiques et Différenciation des Végétaux Cultivés, Bât. SN2, Université Lille 1, F-59655 Villeneuve d'Ascq, France
| | - Godfrey Neutelings
- UMR INRA-USTL 1281 Stress Abiotiques et Différenciation des Végétaux Cultivés, Bât. SN2, Université Lille 1, F-59655 Villeneuve d'Ascq, France
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